More reading material \o/ ere is stated, that MAC-48 is just a historical term for the EUI-48: http://standards.ieee.org/develop/regauth/tut/eui.pdf (page 2). Also: your quoted link only states the handling of the padding.
As far as I see it, only IETF documents speak of the bit-flipping in direct relations to the IPv6 IID, thus we should leave it to the IP layer to toggle the bit (as it already does for "normal" EUI-64, as stated on http://tools.ietf.org/html/rfc4291#page-20).